Two US Navy pilots were shot down over the Red Sea earlier in "an apparent case of friendly fire," the US military said.
Yemen's Iran-backed Huthi rebels said later they had "targeted" the aircraft carrier USS Harry S Truman a day earlier in an operation that led to "shooting down an F-18 aircraft" and thwarting "American-British aggression" against Yemen.
United States Central Command (CENTCOM) said that both US pilots were recovered alive but "initial assessments indicate that one of the crew members sustained minor injuries".
This incident, "was not the result of hostile fire, and a full investigation is underway," CENTCOM said.
The potentially disastrous mistake underscores the dangers of a mission the US has been involved in for more than a year to counter Yemen's Huthi rebels.
The Huthis have repeatedly targeted merchant vessels in the Red Sea and Gulf of Aden, waterways vital to global trade.
They say they are acting in solidarity with Palestinians in Gaza
CENTCOM said the guided missile cruiser USS Gettysburg "mistakenly fired on and hit the F/A-18" fighter aircraft, which Navy pilots had flown off the USS Harry S Truman.
Netanyahu vows to act with 'force' against Yemen's Huthis
Meanwhile, Israeli Prime Minister Benjamin Netanyahu has said that Israel would act firmly against the Huthi rebels in Yemen, a day after the group fired a missile that injured 16 people in Tel Aviv.
"As we acted with force against the terrorist arms of Iran's axis of evil, so we will act against the Huthis... with force, determination and sophistication," Mr Netanyahu said in a video statement.
The US said it conducted strikes on Houthi targets in Yemen's rebel held capital Sanaa, including on what it said was a missile storage centre and a "command-and-control facility".
During the operation, forces also shot down multiple Houthi drones and an anti-ship cruise missile over the Red Sea.
In a statement, CENTCOM said its forces conducted "deliberate strikes to disrupt and degrade Houthi operations, such as attacks against US Navy warships and merchant vessels.
"The strike reflects CENTCOM's ongoing commitment to protect US and coalition personnel, regional partners and international shipping."
The strikes on shipping by the Houthis, who have also launched missiles at Israel, have prompted retaliatory strikes by the United States and Britain.
The US attack on Sanaa comes hours after Houthi missile struck Tel Aviv, wounding 16 people in the second such strike in days.
In a statement, the Houthi rebels pledged to continue their attacks against Israel "until the aggression stops and the siege on the Gaza Strip is lifted".
